Interaction analysis for molecular structures and ensembles

Computing contact fingerprints from a set of static structures

The following steps will generate a contact fingerprint for a set of static structures (e.g. PDB-files solved with X-ray crystallography).


Given two PDB-files of different molecules,

For each structure, first generate a contact list and then the set of residue contact frequencies: --structure structure_1.pdb --itypes hb --output contacts_1.tsv --structure structure_2.pdb --itypes hb --output contacts_2.tsv --input_files contacts_1.tsv --itypes all --output_file resfrequencies_1.tsv --input_files contacts_2.tsv --itypes all --output_file resfrequencies_2.tsv

Next, the residue contact frequencies are combined a plot is written to a png file: --input_frequencies resfrequencies_1.tsv resfrequencies_2.tsv \
                              --column_headers "Structure 1" "Structure 2" \
                              --plot_output fingerprint.png